IPKM/mdevaluate
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  • 32e3541c4b Changed type hint for version from int to str Sebastian Kloth 2023-12-26 16:40:43 +01:00
  • e91de71787 Combined selector and multi_selector in shifted_correlation and added type hints Sebastian Kloth 2023-12-26 16:38:55 +01:00
  • 476f7167b4 Moved functions around to circumvent a circular import Sebastian Kloth 2023-12-26 16:06:38 +01:00
  • cedfd24bb3 Updated regex test for atom_subsets Sebastian Kloth 2023-12-26 16:05:42 +01:00
  • cc185546d6 Small changes to type hints Sebastian Kloth 2023-12-26 15:24:01 +01:00
  • eed94cfca6 Added type hints, adjusted imports, and doc strings Sebastian Kloth 2023-12-26 12:55:53 +01:00
  • c00fc78f23 Added type hints, moved imports and classes around Sebastian Kloth 2023-12-26 11:50:16 +01:00
  • 8bad2861fa Updated doc strings and added type hints Sebastian Kloth 2023-12-26 11:33:59 +01:00
  • aca9ba0723 Updated doc strings and added type hints Sebastian Kloth 2023-12-26 11:29:21 +01:00
  • 2615798088 Added dnn to next_neighbors Sebastian Kloth 2023-12-26 11:07:30 +01:00
  • 97e29e6de3 Refactored next_neighbors and added type hints Sebastian Kloth 2023-12-26 11:05:16 +01:00
  • fd60cae3b8 Added type hints for return values Sebastian Kloth 2023-12-26 11:04:17 +01:00
  • f48e037936 Started rewriting, adding type hints Sebastian Kloth 2023-12-22 14:22:25 +01:00
  • 2d7905315d Added cleanup_h5 to utils.py Sebastian Kloth 2023-12-21 16:39:30 +01:00
  • 21dcc7641b Adjusted van_hove_self to better work with shifted_correlation Sebastian Kloth 2023-12-18 17:02:22 +01:00
  • 62705da6f3 Moved files and reformatted some Sebastian Kloth 2023-12-18 14:47:22 +01:00
  • e91defdc7a Added range for van Hove histogram Sebastian Kloth 2023-12-13 13:49:47 +01:00
  • 43ac510e7d renamed time from time package to pytime Sebastian Kloth 2023-12-09 15:52:15 +01:00
  • c40ea052b8 Added new function for calculating the occupation matrix Sebastian Kloth 2023-12-08 17:20:06 +01:00
  • 5267f6abac Updated version Sebastian Kloth 2023-12-06 15:47:20 +01:00
  • b4486ff265 Added slices to CoordinatesMap Sebastian Kloth 2023-12-06 15:44:33 +01:00
  • 4efb221a80 Reworked while loops to for loops in free_energy_landscape.py Sebastian Kloth 2023-12-06 15:38:15 +01:00
  • fa2e793354 Added test for get_fel Sebastian Kloth 2023-12-06 10:55:55 +01:00
  • d8154d3c38 Initial commit of free_energy_landscape Sebastian Kloth 2023-12-05 17:08:57 +01:00
  • 9b45a1a7bd Applied black formatter Sebastian Kloth 2023-12-05 16:44:26 +01:00
  • a7da9d7ec8 Merge remote-tracking branch 'origin/mdeval_dev' into mdeval_dev Sebastian Kloth 2023-11-19 12:19:06 +01:00
  • ab3d9497d9 Added NoSuchNodeError to except in load_and_concat_data Sebastian Kloth 2023-11-19 12:18:52 +01:00
  • 57a492cb48 Fixed normal_vectors() and removed old pbc_diff Sebastian Kloth 2023-11-13 16:26:06 +01:00
  • a4c365c4a1 Fixed bug in vectors() Sebastian Kloth 2023-11-12 17:37:15 +01:00
  • 2904d1e4d8 Removed cached from open Sebastian Kloth 2023-11-10 15:19:44 +01:00
  • a75091aa95 Adjusted type hint for load_and_concat_data Sebastian Kloth 2023-11-07 11:28:12 +01:00
  • 1a8134c002 Added function to load data for multiply MDSystem Sebastian Kloth 2023-11-07 10:25:29 +01:00
  • 6a7027bb34 Added missing functions from mdeval_skloth Sebastian Kloth 2023-11-06 16:34:43 +01:00
  • 118ed8e6af Added missing functions from mdeval_skloth Sebastian Kloth 2023-11-06 15:53:56 +01:00
  • 9c253a2f58 Added test trajectory offset files to .gitignore Sebastian Kloth 2023-11-06 11:48:57 +01:00
  • cf28882418 Removed CachedReader Sebastian Kloth 2023-11-05 19:39:02 +01:00
  • 1aa5eed106 Moved functions from mdeval_skloth and removed deprecated code Sebastian Kloth 2023-11-05 15:06:28 +01:00
  • 4b139db471 Moved package files to src Sebastian Kloth 2023-11-05 12:01:26 +01:00
  • 22287d167d Fixed shear correction in pbc_points Sebastian Kloth 2023-10-18 15:33:19 +02:00
  • 5aec83b358 Removed unused imports Sebastian Kloth 2023-10-13 16:53:10 +02:00
  • 9cbdd2b464 Fixed vectors to take box of each frame Sebastian Kloth 2023-09-26 16:23:14 +02:00
  • b17aa6b199 Merge remote-tracking branch 'origin/main' Sebastian Kloth 2023-09-16 13:40:12 +02:00
  • ec791ece8b Changed energy file reader to output a DataFrame Sebastian Kloth 2023-09-16 13:40:02 +02:00
  • 9fec40521e Exchanged setup.py with pyproject.toml Sebastian Kloth 2023-07-24 11:49:48 +02:00
  • 69715fd2a7 Added multi_selector to shifted_correlation. Sebastian Kloth 2023-07-22 11:57:17 +02:00
  • bc078f890b Changed requirements Sebastian Kloth 2023-07-03 13:23:15 +02:00
  • ef2a3b9f40 Changed LICENSE sebastiankloth 2023-06-30 14:28:37 +02:00
  • f453aa6fa0 Removed except clause in shifted_correlation to always raise an exception. sebastiankloth 2023-06-30 08:58:36 +02:00
  • 2125c4de47 Fix for shear sims in pbc_points sebastiankloth 2023-06-29 09:37:42 +02:00
  • 3f4f155976 Added a comment for the latest change in pbc_points. sebastiankloth 2023-06-28 13:55:38 +02:00
  • 76e44dde49 Changed pbc_points to allow to shift the box in the other direction for shear simulations. sebastiankloth 2023-06-28 13:53:37 +02:00
  • 8146a9b270 Readded the try except block to shifted_correlation. sebastiankloth 2023-06-27 17:29:36 +02:00
  • a1d0cee510 Changed open_energy to use MDAnalysis instead of Gromacs energy tool. sebastiankloth 2023-06-27 11:25:29 +02:00
  • f6416756a3 Changed energy_reader to use MDAnalysis instead of Gromacs energy tool. sebastiankloth 2023-06-27 10:58:15 +02:00
  • 578d3638a4 Removed delayed reader. sebastiankloth 2023-06-27 10:35:15 +02:00
  • ef125c2a89 Used black for formatting. sebastiankloth 2023-06-27 10:26:23 +02:00
  • a2164507d5 Added possibility to use more images with pbc_points. sebastiankloth 2023-06-21 13:03:05 +02:00
  • a4b1105c54 Removed try except block from shifted_correlation. sebastiankloth 2023-06-16 08:41:19 +02:00
  • f83b0c0cfb Changed requirement.txt sebastiankloth 2023-04-20 14:43:07 +02:00
  • d89c903e5d Nojump matrix is now saved in data when trajectory dir is not writable sebastiankloth 2023-04-20 13:35:10 +02:00
  • 78f0b3d727 Changed to load own nojump matrix first if not owner of trajectory sebastiankloth 2023-04-20 11:50:42 +02:00
  • eaacdbf4ad Modified .gitignore sebastiankloth 2023-02-22 11:07:29 +01:00
  • 57f0a23e00 Fixed shiftetd correlation for 1 node sebastiankloth 2023-01-23 11:06:20 +01:00
  • e321c94c41 Changed error print into logger.warning sebastiankloth 2022-11-04 11:17:53 +01:00
  • 8cdfb7a0dd Updated requirements.txt sebastiankloth 2022-11-04 11:00:26 +01:00
  • 88e4fb964b Added docu to hbonds sebastiankloth 2022-11-04 08:46:31 +01:00
  • a38e601fcb Adjusted functions to work with new pbc_poits sebastiankloth 2022-11-03 16:20:04 +01:00
  • 0bd82ee281 Changed pbc_poits to general case sebastiankloth 2022-11-03 16:05:22 +01:00
  • 4d257b00ee Added hbonds function sebastiankloth 2022-11-03 15:46:14 +01:00
  • 3992dd4e07 Changed shifted_correlation to support parallelization and easy input of selectors sebastiankloth 2022-11-03 15:42:58 +01:00
  • 9628053d26 Changed whole to only support simple sebastiankloth 2022-11-03 15:34:48 +01:00
  • eea3973cda Changed version to 22.11 sebastiankloth 2022-11-03 14:17:49 +01:00
  • 33db65b148 Changed autosave sebastiankloth 2022-11-03 14:17:28 +01:00
  • 36eddfff1c Added allow_pickle in autosave_data sebastiankloth 2022-06-09 08:53:58 +02:00
  • 93686c1361 Added allow_pickle in autosave_data sebastiankloth 2022-06-09 08:35:49 +02:00
  • cfe7b9db4c Increased version sebastiankloth 2022-06-08 15:12:59 +02:00
  • b2ce71cbdd Allow pickle for autosave sebastiankloth 2022-06-08 14:28:09 +02:00
  • 39bccf8792 Changed energy_reader genfromtxt to loadtxt sebastiankloth 2022-05-25 16:39:41 +02:00
  • 94a30b1d40 Changed requirements sebastiankloth 2022-05-25 10:03:30 +02:00
  • fc975aef0c add option to specify charges and masses for .gro files sebastiankloth 2022-05-05 10:58:37 +02:00
  • dee05b44f6 changed version sebastiankloth 2022-05-05 10:25:53 +02:00
  • aee6e33d75 Changed version sebastiankloth 2022-05-03 15:18:28 +02:00
  • c18a369473 Fixed index reader sebastiankloth 2022-05-03 15:15:12 +02:00
  • 6c54848105 Reimplemented index reader sebastiankloth 2022-05-02 17:20:34 +02:00
  • cefdcf7e21 Removed backups from energy reader sebastiankloth 2022-04-27 15:38:49 +02:00
  • 82c9b9ee36 Added import for pandas sebastiankloth 2022-04-27 15:37:08 +02:00
  • 1a263632b3 Added import for re sebastiankloth 2022-04-27 15:27:31 +02:00
  • d064d8c963 Added import for subprocess sebastiankloth 2022-04-27 15:14:02 +02:00
  • a2ae4ebfb2 Changed version sebastiankloth 2022-04-27 15:13:18 +02:00
  • 635cd51f7a Changed version sebastiankloth 2022-04-27 14:23:08 +02:00
  • 36a5d02b8c Adden new reader for energy files sebastiankloth 2022-04-27 14:16:04 +02:00
  • 68b8e1a305 Initial version sebastiankloth 2022-04-20 14:08:38 +02:00